pymatgen.electronic_structure.plotter module
This module implements plotter for DOS and band structure.
- class BSDOSPlotter(bs_projection: Literal['elements'] | None = 'elements', dos_projection: str = 'elements', vb_energy_range: float = 4, cb_energy_range: float = 4, fixed_cb_energy: bool = False, egrid_interval: float = 1, font: str = 'Times New Roman', axis_fontsize: float = 20, tick_fontsize: float = 15, legend_fontsize: float = 14, bs_legend: str = 'best', dos_legend: str = 'best', rgb_legend: bool = True, fig_size: tuple[float, float] = (11, 8.5))[source]
Bases:
object
A joint, aligned band structure and density of states plot. Contributions from Jan Pohls as well as the online example from Germain Salvato-Vallverdu: http://gvallver.perso.univ-pau.fr/?p=587
Instantiate plotter settings.
- Parameters:
bs_projection ('elements' | None) – Whether to project the bands onto elements.
dos_projection (str) – “elements”, “orbitals”, or None
vb_energy_range (float) – energy in eV to show of valence bands
cb_energy_range (float) – energy in eV to show of conduction bands
fixed_cb_energy (bool) – If true, the cb_energy_range will be interpreted as constant (i.e., no gap correction for cb energy)
egrid_interval (float) – interval for grid marks
font (str) – font family
axis_fontsize (float) – font size for axis
tick_fontsize (float) – font size for axis tick labels
legend_fontsize (float) – font size for legends
bs_legend (str) – matplotlib string location for legend or None
dos_legend (str) – matplotlib string location for legend or None
rgb_legend (bool) – (T/F) whether to draw RGB triangle/bar for element proj.
fig_size (tuple) – dimensions of figure size (width, height)
- get_plot(bs: BandStructureSymmLine, dos: Dos | CompleteDos | None = None)[source]
Get a matplotlib plot object.
- Parameters:
bs (BandStructureSymmLine) – the bandstructure to plot. Projection data must exist for projected plots.
dos (Dos) – the Dos to plot. Projection data must exist (i.e., CompleteDos) for projected plots.
- Returns:
matplotlib.pyplot object on which you can call commands like show() and savefig()
- class BSPlotter(bs: BandStructureSymmLine)[source]
Bases:
object
Class to plot or get data to facilitate the plot of band structure objects.
- Parameters:
bs – A BandStructureSymmLine object.
- add_bs(bs: BandStructureSymmLine | list[BandStructureSymmLine]) None [source]
Method to add bands objects to the BSPlotter
- bs_plot_data(zero_to_efermi=True, bs=None, bs_ref=None, split_branches=True)[source]
Get the data nicely formatted for a plot
- Parameters:
zero_to_efermi – Automatically set the Fermi level as the plot’s origin (i.e. subtract E - E_f). Defaults to True.
bs – the bandstructure to get the data from. If not provided, the first one in the self._bs list will be used.
bs_ref – is the bandstructure of reference when a rescale of the distances is need to plot multiple bands
split_branches – if True distances and energies are split according to the branches. If False distances and energies are split only where branches are discontinuous (reducing the number of lines to plot).
- Returns:
A dictionary of the following format: ticks: A dict with the ‘distances’ at which there is a kpoint (the x axis) and the labels (None if no label). energy: A dict storing bands for spin up and spin down data {Spin:[np.array(nb_bands,kpoints),…]} as a list of discontinuous kpath of energies. The energy of multiple continuous branches are stored together. vbm: A list of tuples (distance,energy) marking the vbms. The energies are shifted with respect to the fermi level is the option has been selected. cbm: A list of tuples (distance,energy) marking the cbms. The energies are shifted with respect to the fermi level is the option has been selected. lattice: The reciprocal lattice. zero_energy: This is the energy used as zero for the plot. band_gap:A string indicating the band gap and its nature (empty if it’s a metal). is_metal: True if the band structure is metallic (i.e., there is at least one band crossing the fermi level).
- Return type:
dict
- get_plot(zero_to_efermi=True, ylim=None, smooth=False, vbm_cbm_marker=False, smooth_tol=0, smooth_k=3, smooth_np=100, bs_labels=None)[source]
Get a matplotlib object for the bandstructures plot. Multiple bandstructure objs are plotted together if they have the same high symm path.
- Parameters:
zero_to_efermi – Automatically set the Fermi level as the plot’s origin (i.e. subtract E - E_f). Defaults to True.
ylim – Specify the y-axis (energy) limits; by default None let the code choose. It is vbm-4 and cbm+4 if insulator efermi-10 and efermi+10 if metal
smooth (bool or list(bools)) – interpolates the bands by a spline cubic. A single bool values means to interpolate all the bandstructure objs. A list of bools allows to select the bandstructure obs to interpolate.
vbm_cbm_marker (bool) – if True, a marker is added to the vbm and cbm.
smooth_tol (float) – tolerance for fitting spline to band data. Default is None such that no tolerance will be used.
smooth_k (int) – degree of splines 1<k<5
smooth_np (int) – number of interpolated points per each branch.
bs_labels – labels for each band for the plot legend.
- get_ticks()[source]
Get all ticks and labels for a band structure plot.
- Returns:
A dictionary with ‘distance’: a list of distance at which ticks should be set and ‘label’: a list of label for each of those ticks.
- Return type:
dict
- get_ticks_old()[source]
Get all ticks and labels for a band structure plot.
- Returns:
A dictionary with ‘distance’: a list of distance at which ticks should be set and ‘label’: a list of label for each of those ticks.
- Return type:
dict
- plot_compare(other_plotter, legend=True)[source]
Plot two band structure for comparison. One is in red the other in blue (no difference in spins). The two band structures need to be defined on the same symmetry lines! and the distance between symmetry lines is the one of the band structure used to build the BSPlotter
- Parameters:
other_plotter – Another band structure object defined along the same symmetry lines
legend – True to add a legend to the plot
- Returns:
a matplotlib object with both band structures
- save_plot(filename, img_format='eps', ylim=None, zero_to_efermi=True, smooth=False)[source]
Save matplotlib plot to a file.
- Parameters:
filename – Filename to write to.
img_format – Image format to use. Defaults to EPS.
ylim – Specifies the y-axis limits.
zero_to_efermi – Automatically set the Fermi level as the plot’s origin (i.e. subtract E - E_f). Defaults to True.
smooth – Cubic spline interpolation of the bands.
- show(zero_to_efermi=True, ylim=None, smooth=False, smooth_tol=None)[source]
Show the plot using matplotlib.
- Parameters:
zero_to_efermi – Automatically set the Fermi level as the plot’s origin (i.e. subtract E - E_f). Defaults to True.
ylim – Specify the y-axis (energy) limits; by default None let the code choose. It is vbm-4 and cbm+4 if insulator efermi-10 and efermi+10 if metal
smooth – interpolates the bands by a spline cubic
smooth_tol (float) – tolerance for fitting spline to band data. Default is None such that no tolerance will be used.
- class BSPlotterProjected(bs)[source]
Bases:
BSPlotter
Class to plot or get data to facilitate the plot of band structure objects projected along orbitals, elements or sites.
- Parameters:
bs – A BandStructureSymmLine object with projections.
- get_elt_projected_plots(zero_to_efermi=True, ylim=None, vbm_cbm_marker=False)[source]
Method returning a plot composed of subplots along different elements
- Returns:
a pylab object with different subfigures for each projection The blue and red colors are for spin up and spin down The bigger the red or blue dot in the band structure the higher character for the corresponding element and orbital
- get_elt_projected_plots_color(zero_to_efermi=True, elt_ordered=None)[source]
Returns a pylab plot object with one plot where the band structure line color depends on the character of the band (along different elements). Each element is associated with red, green or blue and the corresponding rgb color depending on the character of the band is used. The method can only deal with binary and ternary compounds
spin up and spin down are differientiated by a ‘-’ and a ‘–’ line
- Parameters:
zero_to_efermi – Automatically set the Fermi level as the plot’s origin (i.e. subtract E - E_f). Defaults to True.
elt_ordered – A list of Element ordered. The first one is red, second green, last blue
- Returns:
a pylab object
- get_projected_plots_dots(dictio, zero_to_efermi=True, ylim=None, vbm_cbm_marker=False)[source]
Method returning a plot composed of subplots along different elements and orbitals.
- Parameters:
dictio – The element and orbitals you want a projection on. The format is {Element:[Orbitals]} for instance {‘Cu’:[‘d’,’s’],’O’:[‘p’]} will give projections for Cu on d and s orbitals and on oxygen p. If you use this class to plot LobsterBandStructureSymmLine, the orbitals are named as in the FATBAND filename, e.g. “2p” or “2p_x”
zero_to_efermi – Automatically set the Fermi level as the plot’s origin (i.e. subtract E - E_f). Defaults to True.
ylim – Specify the y-axis limits. Defaults to None.
vbm_cbm_marker – Add markers for the VBM and CBM. Defaults to False.
- Returns:
a pylab object with different subfigures for each projection The blue and red colors are for spin up and spin down. The bigger the red or blue dot in the band structure the higher character for the corresponding element and orbital.
- get_projected_plots_dots_patom_pmorb(dictio, dictpa, sum_atoms=None, sum_morbs=None, zero_to_efermi=True, ylim=None, vbm_cbm_marker=False, selected_branches=None, w_h_size=(12, 8), num_column=None)[source]
Method returns a plot composed of subplots for different atoms and orbitals (subshell orbitals such as ‘s’, ‘p’, ‘d’ and ‘f’ defined by azimuthal quantum numbers l = 0, 1, 2 and 3, respectively or individual orbitals like ‘px’, ‘py’ and ‘pz’ defined by magnetic quantum numbers m = -1, 1 and 0, respectively). This is an extension of “get_projected_plots_dots” method.
- Parameters:
dictio – The elements and the orbitals you need to project on. The format is {Element:[Orbitals]}, for instance: {‘Cu’:[‘dxy’,’s’,’px’],’O’:[‘px’,’py’,’pz’]} will give projections for Cu on orbitals dxy, s, px and for O on orbitals px, py, pz. If you want to sum over all individual orbitals of subshell orbitals, for example, ‘px’, ‘py’ and ‘pz’ of O, just simply set {‘Cu’:[‘dxy’,’s’,’px’],’O’:[‘p’]} and set sum_morbs (see explanations below) as {‘O’:[p],…}. Otherwise, you will get an error.
dictpa – The elements and their sites (defined by site numbers) you need to project on. The format is {Element: [Site numbers]}, for instance: {‘Cu’:[1,5],’O’:[3,4]} will give projections for Cu on site-1 and on site-5, O on site-3 and on site-4 in the cell. The correct site numbers of atoms are consistent with themselves in the structure computed. Normally, the structure should be totally similar with POSCAR file, however, sometimes VASP can rotate or translate the cell. Thus, it would be safe if using Vasprun class to get the final_structure and as a result, correct index numbers of atoms.
sum_atoms –
Sum projection of the similar atoms together (e.g.: Cu on site-1 and Cu on site-5). The format is {Element: [Site numbers]}, for instance:
{‘Cu’: [1,5], ‘O’: [3,4]} means summing projections over Cu on site-1 and Cu on site-5 and O on site-3 and on site-4. If you do not want to use this functional, just turn it off by setting sum_atoms = None.
sum_morbs – Sum projections of individual orbitals of similar atoms together (e.g.: ‘dxy’ and ‘dxz’). The format is {Element: [individual orbitals]}, for instance: {‘Cu’: [‘dxy’, ‘dxz’], ‘O’: [‘px’, ‘py’]} means summing projections over ‘dxy’ and ‘dxz’ of Cu and ‘px’ and ‘py’ of O. If you do not want to use this functional, just turn it off by setting sum_morbs = None.
zero_to_efermi – Automatically set the Fermi level as the plot’s origin (i.e. subtract E - E_f). Defaults to True.
ylim – The y-axis limit. Defaults to None.
vbm_cbm_marker – Whether to plot points to indicate valence band maxima and conduction band minima positions. Defaults to False.
selected_branches – The index of symmetry lines you chose for plotting. This can be useful when the number of symmetry lines (in KPOINTS file) are manny while you only want to show for certain ones. The format is [index of line], for instance: [1, 3, 4] means you just need to do projection along lines number 1, 3 and 4 while neglecting lines number 2 and so on. By default, this is None type and all symmetry lines will be plotted.
w_h_size – This variable help you to control the width and height of figure. By default, width = 12 and height = 8 (inches). The width/height ratio is kept the same for subfigures and the size of each depends on how many number of subfigures are plotted.
num_column – This variable help you to manage how the subfigures are arranged in the figure by setting up the number of columns of subfigures. The value should be an int number. For example, num_column = 3 means you want to plot subfigures in 3 columns. By default, num_column = None and subfigures are aligned in 2 columns.
- Returns:
A pylab object with different subfigures for different projections. The blue and red colors lines are bands for spin up and spin down. The green and cyan dots are projections for spin up and spin down. The bigger the green or cyan dots in the projected band structures, the higher character for the corresponding elements and orbitals. List of individual orbitals and their numbers (set up by VASP and no special meaning): s = 0; py = 1 pz = 2 px = 3; dxy = 4 dyz = 5 dz2 = 6 dxz = 7 dx2 = 8; f_3 = 9 f_2 = 10 f_1 = 11 f0 = 12 f1 = 13 f2 = 14 f3 = 15
- class BoltztrapPlotter(bz)[source]
Bases:
object
class containing methods to plot the data from Boltztrap.
- Parameters:
bz – a BoltztrapAnalyzer object
- plot_carriers(temp=300)[source]
Plot the carrier concentration in function of Fermi level
- Parameters:
temp – the temperature
- Returns:
a matplotlib object
- plot_complexity_factor_mu(temps=(300,), output='average', Lambda=0.5)[source]
Plot respect to the chemical potential of the Fermi surface complexity factor calculated as explained in Ref. Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor from ab initio band structure calculations. npj Computational Materials 3, 8 (2017).
- Parameters:
output – ‘average’ returns the complexity factor calculated using the average of the three diagonal components of the seebeck and conductivity tensors. ‘tensor’ returns the complexity factor respect to the three diagonal components of seebeck and conductivity tensors.
temps – list of temperatures of calculated seebeck and conductivity.
Lambda – fitting parameter used to model the scattering (0.5 means constant relaxation time).
- Returns:
a matplotlib object
- plot_conductivity_dop(temps='all', output='average', relaxation_time=1e-14)[source]
Plot the conductivity in function of doping levels for different temperatures.
- Parameters:
temps – the default ‘all’ plots all the temperatures in the analyzer. Specify a list of temperatures if you want to plot only some.
output – with ‘average’ you get an average of the three directions with ‘eigs’ you get all the three directions.
relaxation_time – specify a constant relaxation time value
- Returns:
a matplotlib object
- plot_conductivity_mu(temp: float = 600, output: str = 'eig', relaxation_time: float = 1e-14, xlim: Sequence[float] | None = None)[source]
Plot the conductivity in function of Fermi level. Semi-log plot
- Parameters:
temp (float) – the temperature
output (str) – “eig” or “average”
relaxation_time (float) – A relaxation time in s. Defaults to 1e-14 and the plot is in units of relaxation time
xlim (tuple[float, float]) – a 2-tuple of min and max fermi energy. Defaults to (0, band gap)
- Returns:
a matplotlib object
- plot_conductivity_temp(doping='all', output='average', relaxation_time=1e-14)[source]
Plot the conductivity in function of temperature for different doping levels.
- Parameters:
doping (str) – the default ‘all’ plots all the doping levels in the analyzer. Specify a list of doping levels if you want to plot only some.
output – with ‘average’ you get an average of the three directions with ‘eigs’ you get all the three directions.
relaxation_time – specify a constant relaxation time value
- Returns:
a matplotlib object
- plot_eff_mass_dop(temps='all', output='average')[source]
Plot the average effective mass in function of doping levels for different temperatures.
- Parameters:
temps – the default ‘all’ plots all the temperatures in the analyzer. Specify a list of temperatures if you want to plot only some.
output – with ‘average’ you get an average of the three directions with ‘eigs’ you get all the three directions.
relaxation_time – specify a constant relaxation time value
- Returns:
a matplotlib object
- plot_eff_mass_temp(doping='all', output='average')[source]
Plot the average effective mass in function of temperature for different doping levels.
- Parameters:
doping (str) – the default ‘all’ plots all the doping levels in the analyzer. Specify a list of doping levels if you want to plot only some.
output – with ‘average’ you get an average of the three directions with ‘eigs’ you get all the three directions.
- Returns:
a matplotlib object
- plot_hall_carriers(temp=300)[source]
Plot the Hall carrier concentration in function of Fermi level
- Parameters:
temp – the temperature
- Returns:
a matplotlib object
- plot_power_factor_dop(temps='all', output='average', relaxation_time=1e-14)[source]
Plot the Power Factor in function of doping levels for different temperatures.
- Parameters:
temps – the default ‘all’ plots all the temperatures in the analyzer. Specify a list of temperatures if you want to plot only some.
output – with ‘average’ you get an average of the three directions with ‘eigs’ you get all the three directions.
relaxation_time – specify a constant relaxation time value
- Returns:
a matplotlib object
- plot_power_factor_mu(temp: float = 600, output: str = 'eig', relaxation_time: float = 1e-14, xlim: Sequence[float] | None = None)[source]
Plot the power factor in function of Fermi level. Semi-log plot
- Parameters:
temp (float) – the temperature
output (str) – “eig” or “average”
relaxation_time (float) – A relaxation time in s. Defaults to 1e-14 and the plot is in units of relaxation time
xlim (tuple[float, float]) – a 2-tuple of min and max fermi energy. Defaults to (0, band gap)
- Returns:
a matplotlib object
- plot_power_factor_temp(doping='all', output='average', relaxation_time=1e-14)[source]
Plot the Power Factor in function of temperature for different doping levels.
- Parameters:
doping (str) – the default ‘all’ plots all the doping levels in the analyzer. Specify a list of doping levels if you want to plot only some.
output – with ‘average’ you get an average of the three directions with ‘eigs’ you get all the three directions.
relaxation_time – specify a constant relaxation time value
- Returns:
a matplotlib object
- plot_seebeck_dop(temps='all', output='average')[source]
Plot the Seebeck in function of doping levels for different temperatures.
- Parameters:
temps – the default ‘all’ plots all the temperatures in the analyzer. Specify a list of temperatures if you want to plot only some.
output – with ‘average’ you get an average of the three directions with ‘eigs’ you get all the three directions.
- Returns:
a matplotlib object
- plot_seebeck_eff_mass_mu(temps=(300,), output='average', Lambda=0.5)[source]
Plot respect to the chemical potential of the Seebeck effective mass calculated as explained in Ref. Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor from ab initio band structure calculations. npj Computational Materials 3, 8 (2017).
- Parameters:
output – ‘average’ returns the seebeck effective mass calculated using the average of the three diagonal components of the seebeck tensor. ‘tensor’ returns the seebeck effective mass respect to the three diagonal components of the seebeck tensor.
temps – list of temperatures of calculated seebeck.
Lambda – fitting parameter used to model the scattering (0.5 means constant relaxation time).
- Returns:
a matplotlib object
- plot_seebeck_mu(temp: float = 600, output: str = 'eig', xlim: Sequence[float] | None = None)[source]
Plot the seebeck coefficient in function of Fermi level
- Parameters:
temp (float) – the temperature
output (str) – “eig” or “average”
xlim (tuple[float, float]) – a 2-tuple of min and max fermi energy. Defaults to (0, band gap)
- Returns:
a matplotlib object
- plot_seebeck_temp(doping='all', output='average')[source]
Plot the Seebeck coefficient in function of temperature for different doping levels.
- Parameters:
doping (str) – the default ‘all’ plots all the doping levels in the analyzer. Specify a list of doping levels if you want to plot only some.
output – with ‘average’ you get an average of the three directions with ‘eigs’ you get all the three directions.
- Returns:
a matplotlib object
- plot_zt_dop(temps='all', output='average', relaxation_time=1e-14)[source]
Plot the figure of merit zT in function of doping levels for different temperatures.
- Parameters:
temps – the default ‘all’ plots all the temperatures in the analyzer. Specify a list of temperatures if you want to plot only some.
output – with ‘average’ you get an average of the three directions with ‘eigs’ you get all the three directions.
relaxation_time – specify a constant relaxation time value
- Returns:
a matplotlib object
- plot_zt_mu(temp: float = 600, output: str = 'eig', relaxation_time: float = 1e-14, xlim: Sequence[float] | None = None)[source]
Plot the ZT in function of Fermi level.
- Parameters:
temp (float) – the temperature
output (str) – “eig” or “average”
relaxation_time (float) – A relaxation time in s. Defaults to 1e-14 and the plot is in units of relaxation time
xlim (tuple[float, float]) – a 2-tuple of min and max fermi energy. Defaults to (0, band gap)
- Returns:
matplotlib.pyplot module
- plot_zt_temp(doping='all', output='average', relaxation_time=1e-14)[source]
Plot the figure of merit zT in function of temperature for different doping levels.
- Parameters:
doping (str) – the default ‘all’ plots all the doping levels in the analyzer. Specify a list of doping levels if you want to plot only some.
output – with ‘average’ you get an average of the three directions with ‘eigs’ you get all the three directions.
relaxation_time – specify a constant relaxation time value
- Returns:
a matplotlib object
- class CohpPlotter(zero_at_efermi=True, are_coops=False, are_cobis=False)[source]
Bases:
object
Class for plotting crystal orbital Hamilton populations (COHPs) or crystal orbital overlap populations (COOPs). It is modeled after the DosPlotter object.
- Parameters:
zero_at_efermi – Whether to shift all populations to have zero energy at the Fermi level. Defaults to True.
are_coops – Switch to indicate that these are COOPs, not COHPs. Defaults to False for COHPs.
are_cobis – Switch to indicate that these are COBIs, not COHPs/COOPs. Defaults to False for COHPs
- add_cohp(label, cohp)[source]
Adds a COHP for plotting.
- Parameters:
label – Label for the COHP. Must be unique.
cohp – COHP object.
- add_cohp_dict(cohp_dict, key_sort_func=None)[source]
Adds a dictionary of COHPs with an optional sorting function for the keys.
- Parameters:
cohp_dict – dict of the form {label: Cohp}
key_sort_func – function used to sort the cohp_dict keys.
- get_cohp_dict()[source]
Returns the added COHPs as a json-serializable dict. Note that if you have specified smearing for the COHP plot, the populations returned will be the smeared and not the original populations.
- Returns:
Dict of COHP data of the form {label: {“efermi”: efermi, “energies”: …, “COHP”: {Spin.up: …}, “ICOHP”: …}}.
- Return type:
dict
- get_plot(xlim=None, ylim=None, plot_negative=None, integrated=False, invert_axes=True)[source]
Get a matplotlib plot showing the COHP.
- Parameters:
xlim – Specifies the x-axis limits. Defaults to None for automatic determination.
ylim – Specifies the y-axis limits. Defaults to None for automatic determination.
plot_negative – It is common to plot -COHP(E) so that the sign means the same for COOPs and COHPs. Defaults to None for automatic determination: If are_coops is True, this will be set to False, else it will be set to True.
integrated – Switch to plot ICOHPs. Defaults to False.
invert_axes – Put the energies onto the y-axis, which is common in chemistry.
- Returns:
A matplotlib object.
- save_plot(filename, img_format='eps', xlim=None, ylim=None)[source]
Save matplotlib plot to a file.
- Parameters:
filename – File name to write to.
img_format – Image format to use. Defaults to EPS.
xlim – Specifies the x-axis limits. Defaults to None for automatic determination.
ylim – Specifies the y-axis limits. Defaults to None for automatic determination.
- class DosPlotter(zero_at_efermi: bool = True, stack: bool = False, sigma: float | None = None)[source]
Bases:
object
Class for plotting DOSs. Note that the interface is extremely flexible given that there are many different ways in which people want to view DOS. The typical usage is:
# Initializes plotter with some optional args. Defaults are usually # fine, plotter = DosPlotter() # Adds a DOS with a label. plotter.add_dos("Total DOS", dos) # Alternatively, you can add a dict of DOSs. This is the typical # form returned by CompleteDos.get_spd/element/others_dos(). plotter.add_dos_dict({"dos1": dos1, "dos2": dos2}) plotter.add_dos_dict(complete_dos.get_spd_dos())
- Parameters:
zero_at_efermi (bool) – Whether to shift all Dos to have zero energy at the fermi energy. Defaults to True.
stack (bool) – Whether to plot the DOS as a stacked area graph
sigma (float) – Specify a standard deviation for Gaussian smearing the DOS for nicer looking plots. Defaults to None for no smearing.
- add_dos(label: str, dos: Dos) None [source]
Adds a dos for plotting.
- Parameters:
label – label for the DOS. Must be unique.
dos – Dos object
- add_dos_dict(dos_dict, key_sort_func=None)[source]
Add a dictionary of doses, with an optional sorting function for the keys.
- Parameters:
dos_dict – dict of {label: Dos}
key_sort_func – function used to sort the dos_dict keys.
- get_dos_dict()[source]
Returns the added doses as a json-serializable dict. Note that if you have specified smearing for the DOS plot, the densities returned will be the smeared densities, not the original densities.
- Returns:
Dict of dos data. Generally of the form {label: {‘energies’:…, ‘densities’: {‘up’:…}, ‘efermi’:efermi}}
- Return type:
dict
- get_plot(xlim: tuple[float, float] | None = None, ylim: tuple[float, float] | None = None, invert_axes: bool = False, beta_dashed: bool = False)[source]
Get a matplotlib plot showing the DOS.
- Parameters:
xlim (tuple[float, float]) – The energy axis limits. Defaults to None for automatic determination.
ylim (tuple[float, float]) – The y-axis limits. Defaults to None for automatic determination.
invert_axes (bool) – Whether to invert the x and y axes. Enables chemist style DOS plotting. Defaults to False.
beta_dashed (bool) – Plots the beta spin channel with a dashed line. Defaults to False.
- save_plot(filename, img_format='eps', xlim=None, ylim=None, invert_axes=False, beta_dashed=False)[source]
Save matplotlib plot to a file.
- Parameters:
filename – Filename to write to.
img_format – Image format to use. Defaults to EPS.
xlim – Specifies the x-axis limits. Set to None for automatic determination.
ylim – Specifies the y-axis limits.
invert_axes (bool) – Whether to invert the x and y axes. Enables chemist style DOS plotting. Defaults to False.
beta_dashed (bool) – Plots the beta spin channel with a dashed line. Defaults to False.
- show(xlim=None, ylim=None, invert_axes=False, beta_dashed=False)[source]
Show the plot using matplotlib.
- Parameters:
xlim – Specifies the x-axis limits. Set to None for automatic determination.
ylim – Specifies the y-axis limits.
invert_axes (bool) – Whether to invert the x and y axes. Enables chemist style DOS plotting. Defaults to False.
beta_dashed (bool) – Plots the beta spin channel with a dashed line. Defaults to False.
- fold_point(p, lattice, coords_are_cartesian=False)[source]
Folds a point with coordinates p inside the first Brillouin zone of the lattice.
- Parameters:
p – coordinates of one point
lattice – Lattice object used to convert from reciprocal to Cartesian coordinates
coords_are_cartesian – Set to True if you are providing coordinates in Cartesian coordinates. Defaults to False.
- Returns:
The Cartesian coordinates folded inside the first Brillouin zone
- plot_brillouin_zone(bz_lattice, lines=None, labels=None, kpoints=None, fold=False, coords_are_cartesian=False, ax=None, **kwargs)[source]
Plots a 3D representation of the Brillouin zone of the structure. Can add to the plot paths, labels and kpoints
- Parameters:
bz_lattice – Lattice object of the Brillouin zone
lines – list of lists of coordinates. Each list represent a different path
labels – dict containing the label as a key and the coordinates as value.
kpoints – list of coordinates
fold – whether the points should be folded inside the first Brillouin Zone. Defaults to False. Requires lattice if True.
coords_are_cartesian – Set to True if you are providing coordinates in Cartesian coordinates. Defaults to False.
ax – matplotlib
Axes
or None if a new figure should be created.kwargs – provided by add_fig_kwargs decorator
- Returns:
matplotlib figure
Keyword arguments controlling the display of the figure:
kwargs
Meaning
title
Title of the plot (Default: None).
show
True to show the figure (default: True).
savefig
”abc.png” or “abc.eps” to save the figure to a file.
size_kwargs
Dictionary with options passed to fig.set_size_inches e.g. size_kwargs=dict(w=3, h=4)
tight_layout
True to call fig.tight_layout (default: False)
ax_grid
True (False) to add (remove) grid from all axes in fig. Default: None i.e. fig is left unchanged.
ax_annotate
Add labels to subplots e.g. (a), (b). Default: False
fig_close
Close figure. Default: False.
- plot_brillouin_zone_from_kpath(kpath, ax=None, **kwargs)[source]
- Gives the plot (as a matplotlib object) of the symmetry line path in
the Brillouin Zone.
- Parameters:
kpath (HighSymmKpath) – a HighSymmKPath object
ax – matplotlib
Axes
or None if a new figure should be created.**kwargs – provided by add_fig_kwargs decorator
- Returns:
matplotlib figure
Keyword arguments controlling the display of the figure:
kwargs
Meaning
title
Title of the plot (Default: None).
show
True to show the figure (default: True).
savefig
”abc.png” or “abc.eps” to save the figure to a file.
size_kwargs
Dictionary with options passed to fig.set_size_inches e.g. size_kwargs=dict(w=3, h=4)
tight_layout
True to call fig.tight_layout (default: False)
ax_grid
True (False) to add (remove) grid from all axes in fig. Default: None i.e. fig is left unchanged.
ax_annotate
Add labels to subplots e.g. (a), (b). Default: False
fig_close
Close figure. Default: False.
- plot_ellipsoid(hessian, center, lattice=None, rescale=1.0, ax=None, coords_are_cartesian=False, arrows=False, **kwargs)[source]
Plots a 3D ellipsoid rappresenting the Hessian matrix in input. Useful to get a graphical visualization of the effective mass of a band in a single k-point.
- Parameters:
hessian – the Hessian matrix
center – the center of the ellipsoid in reciprocal coords (Default)
lattice – Lattice object of the Brillouin zone
rescale – factor for size scaling of the ellipsoid
ax – matplotlib
Axes
or None if a new figure should be created.coords_are_cartesian – Set to True if you are providing a center in Cartesian coordinates. Defaults to False.
arrows – whether to plot arrows for the principal axes of the ellipsoid. Defaults to False.
**kwargs – passed to the matplotlib function ‘plot_wireframe’. Color defaults to blue, rstride and cstride default to 4, alpha defaults to 0.2.
- Returns:
matplotlib figure and matplotlib ax
- Example of use:
fig,ax=plot_wigner_seitz(struct.reciprocal_lattice) plot_ellipsoid(hessian,[0.0,0.0,0.0], struct.reciprocal_lattice,ax=ax)
- plot_fermi_surface(data, structure, cbm, energy_levels=None, multiple_figure=True, mlab_figure=None, kpoints_dict=None, colors=None, transparency_factor=None, labels_scale_factor=0.05, points_scale_factor=0.02, interactive=True)[source]
Plot the Fermi surface at specific energy value using Boltztrap 1 FERMI mode.
The easiest way to use this plotter is:
Run boltztrap in ‘FERMI’ mode using BoltztrapRunner,
Load BoltztrapAnalyzer using your method of choice (e.g., from_files)
- Pass in your BoltztrapAnalyzer’s fermi_surface_data as this
function’s data argument.
- Parameters:
data – energy values in a 3D grid from a CUBE file via read_cube_file function, or from a BoltztrapAnalyzer.fermi_surface_data
structure – structure object of the material
energy_levels ([float]) – Energy values for plotting the fermi surface(s) By default 0 eV correspond to the VBM, as in the plot of band structure along symmetry line. Default: One surface, with max energy value + 0.01 eV
cbm (bool) – Boolean value to specify if the considered band is a conduction band or not
multiple_figure (bool) – If True a figure for each energy level will be shown. If False all the surfaces will be shown in the same figure. In this last case, tune the transparency factor.
mlab_figure (mayavi.mlab.figure) – A previous figure to plot a new surface on.
kpoints_dict (dict) – dictionary of kpoints to label in the plot. Example: {“K”:[0.5,0.0,0.5]}, coords are fractional
colors ([tuple]) – Iterable of 3-tuples (r,g,b) of integers to define the colors of each surface (one per energy level). Should be the same length as the number of surfaces being plotted. Example (3 surfaces): colors=[(1,0,0), (0,1,0), (0,0,1)] Example (2 surfaces): colors=[(0, 0.5, 0.5)]
transparency_factor (float) – Values in the range [0,1] to tune the opacity of each surface. Should be one transparency_factor per surface.
labels_scale_factor (float) – factor to tune size of the kpoint labels
points_scale_factor (float) – factor to tune size of the kpoint points
interactive (bool) – if True an interactive figure will be shown. If False a non interactive figure will be shown, but it is possible to plot other surfaces on the same figure. To make it interactive, run mlab.show().
- Returns:
- The mlab plotter and an interactive
figure to control the plot.
- Return type:
((mayavi.mlab.figure, mayavi.mlab))
- Note: Experimental.
Please, double check the surface shown by using some other software and report issues.
- plot_labels(labels, lattice=None, coords_are_cartesian=False, ax=None, **kwargs)[source]
Adds labels to a matplotlib Axes
- Parameters:
labels – dict containing the label as a key and the coordinates as value.
lattice – Lattice object used to convert from reciprocal to Cartesian coordinates
coords_are_cartesian – Set to True if you are providing. coordinates in Cartesian coordinates. Defaults to False. Requires lattice if False.
ax – matplotlib
Axes
or None if a new figure should be created.kwargs – kwargs passed to the matplotlib function ‘text’. Color defaults to blue and size to 25.
- Returns:
matplotlib figure and matplotlib ax
- plot_lattice_vectors(lattice, ax=None, **kwargs)[source]
Adds the basis vectors of the lattice provided to a matplotlib Axes
- Parameters:
lattice – Lattice object
ax – matplotlib
Axes
or None if a new figure should be created.kwargs – kwargs passed to the matplotlib function ‘plot’. Color defaults to green and linewidth to 3.
- Returns:
matplotlib figure and matplotlib ax
- plot_path(line, lattice=None, coords_are_cartesian=False, ax=None, **kwargs)[source]
Adds a line passing through the coordinates listed in ‘line’ to a matplotlib Axes
- Parameters:
line – list of coordinates.
lattice – Lattice object used to convert from reciprocal to Cartesian coordinates
coords_are_cartesian – Set to True if you are providing coordinates in Cartesian coordinates. Defaults to False. Requires lattice if False.
ax – matplotlib
Axes
or None if a new figure should be created.kwargs – kwargs passed to the matplotlib function ‘plot’. Color defaults to red and linewidth to 3.
- Returns:
matplotlib figure and matplotlib ax
- plot_points(points, lattice=None, coords_are_cartesian=False, fold=False, ax=None, **kwargs)[source]
Adds Points to a matplotlib Axes
- Parameters:
points – list of coordinates
lattice – Lattice object used to convert from reciprocal to Cartesian coordinates
coords_are_cartesian – Set to True if you are providing coordinates in Cartesian coordinates. Defaults to False. Requires lattice if False.
fold – whether the points should be folded inside the first Brillouin Zone. Defaults to False. Requires lattice if True.
ax – matplotlib
Axes
or None if a new figure should be created.kwargs – kwargs passed to the matplotlib function ‘scatter’. Color defaults to blue
- Returns:
matplotlib figure and matplotlib ax
- plot_wigner_seitz(lattice, ax=None, **kwargs)[source]
Adds the skeleton of the Wigner-Seitz cell of the lattice to a matplotlib Axes
- Parameters:
lattice – Lattice object
ax – matplotlib
Axes
or None if a new figure should be created.kwargs – kwargs passed to the matplotlib function ‘plot’. Color defaults to black and linewidth to 1.
- Returns:
matplotlib figure and matplotlib ax