ppcodes Package

ppcodes Package

base_parser Module

Base class for parsers

exception abipy.ppcodes.base_parser.ParserError

Bases: Exception

Exceptions raised by Parser objects.

class abipy.ppcodes.base_parser.BaseParser(filepath: str)

Bases: object

Abstract class defining the interface that must be provided by the parsers used to extract results from the output file of a pseudopotential generator a.k.a. ppgen

errors

List of strings with errors reported by the pp generator

warnings

List of strings with the warnings reported by the pp generator.

Error

alias of ParserError

property errors: list[str]

List of strings with possible errors reported by the generator at run-time.

property warnings: list[str]

List of strings with possible errors reported by the generator at run-time.

abstract get_results() → dict

Return the most important results in a dictionary.

abstract get_input_str() → str

Returns a string with the input file.

oncv_parser Module

Classes and functions for parsing the ONCVPSP output file and plotting the results.

class abipy.ppcodes.oncv_parser.GrepResults(data, start, stop)

Bases: tuple

data

Alias for field number 0

start

Alias for field number 1

stop

Alias for field number 2

class abipy.ppcodes.oncv_parser.AePsNamedTuple(ae, ps)

Bases: tuple

ae

Alias for field number 0

ps

Alias for field number 1

class abipy.ppcodes.oncv_parser.ConvData(l, energies, values)

Bases: tuple

energies

Alias for field number 1

l

Alias for field number 0

values

Alias for field number 2

class abipy.ppcodes.oncv_parser.AtanLogDer(l, energies, values)

Bases: tuple

energies

Alias for field number 1

l

Alias for field number 0

values

Alias for field number 2

class abipy.ppcodes.oncv_parser.AtomicLevel(nlk: NlkState, eig: float, occ: float, is_valence: bool)

Bases: object

Stores the energy levels of the AE isolated atom.

nlk: NlkState

eig: float

occ: float

is_valence: bool

class abipy.ppcodes.oncv_parser.OncvParser(filepath: str)

Bases: BaseParser

Object to read and extract data from the output file of oncvpsp.

atsym

Z

nc

nv

iexc

psfile

Example

parser = OncvParser(filename).scan()

# To access data: parser.radial_wavefunctions

# To plot data with matplotlib. p = parser.get_plotter() p.plot_atanlogder_econv()

scan(verbose: int = 0) → OncvParser

Scan the output file, set run_completed attribute.

Raises: self.Error if invalid file.

property is_metapsp: bool

property is_oncvpsp: bool

min_ghost_empty_ha()

lmax()

to_string(verbose: int = 0) → str

String representation.

property relativistic: bool

True if fully-relativistic calculation.

rc_l()

Core radii as a function of l extracted from the output file.

kinerr_nlk()

Dictionary with the error on the kinetic energy indexed by nlk.

potentials()

Dict with radial functions with the non-local and local potentials indexed by l. l = -1 corresponds to the local part (if present).

densities()

Dictionary with charge densities on the radial mesh.

kin_densities()

Dictionary with Kinetic energy densities on the radial mesh.

vtaus()

Dictionary with Vtau ptotentials on the radial mesh.

radial_wfs()

Read and set the radial wavefunctions for the bound states.

Usage:

ae_wfs, ps_wfs = self.radial_wfs.ae, self.radial_wfs.ps

for nlk, ae_wf in ae_wfs.items():

ps_wf, l, k = ps_wfs[nlk], nlk.l, nlk.k

property has_scattering_wfs: bool

True if pp generation included scattering states.

scattering_wfs()

Read and set the scattering wavefunctions.

projectors()

Dict with projector wave functions indexed by nlk.

atan_logders()

Atan of the log derivatives for different l-values.

kene_vs_ecut()

Dict with the convergence of the kinetic energy versus ecut for different l-values.

hints()

Hints for the cutoff energy as provided by oncvpsp.

get_results() → AttrDict

Return the most important results extracted from the output file.

find_string(s: str) → int

Returns the index of the first line containing string s. Raises self.Error if s cannot be found.

get_input_str() → str

String with the ONCVPSP input file.

get_psp8_str() → str | None

Return string with the pseudopotential data in psp8 format. Return None if field is not present.

get_upf_str() → str | None

Return string with the pseudopotential data in upf format. Return None if field is not present.

get_plotter()

Return an instance of OncvPlotter or None

gnuplot() → None

Plot the results with gnuplot. Based on the replot.sh script provided by the oncvpsp code.

get_atomic_levels_df() → DataFrame

Return pandas dataframe with the atomic levels. Columns: (n, l, k, eig, occ, is_valence)

get_peaks_df() → DataFrame

Return pandas dataframe with the position of the last peak.

oncv_plotter Module

Classes and functions for parsing the ONCVPSP output file and plotting the results.

class abipy.ppcodes.oncv_plotter.OncvPlotter(parser: OncvParser)

Bases: NotebookWriter

Plots the results produced by a pseudopotential generator.

linewidth = 2

markersize = 2

linestyle_aeps = {'ae': 'solid', 'ps': 'dashed'}

markers_aeps = {'ae': '.', 'ps': 'o'}

color_l = {-3: 'yellow', -2: 'cyan', -1: 'magenta', 0: 'black', 1: 'red', 2: 'blue', 3: 'orange'}

classmethod from_file(filepath: str) → OncvPlotter

Build the plotter from an output file.

static decorate_ax(ax, xlabel=None, ylabel=None, title=None, fontsize=8)

Decorate a matplotlib Axis adding xlabel, ylabel, title, grid and legend

plot_atan_logders(ax=None, with_xlabel=True, fontsize: int = 8, **kwargs) → Any

Plot arctan of logder on axis ax.

Parameters:

ax – matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_radial_wfs(ax=None, what='bound_states', fontsize: int = 8, **kwargs) → Any

Plot AE and PS radial wavefunctions on axis ax.

Parameters:

• ax – matplotlib.axes.Axes or None if a new figure should be created.

• what – “bound_states” or “scattering_states”.

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.
plotly	Try to convert mpl figure to plotly.

plot_projectors(ax=None, fontsize: int = 8, **kwargs) → Any

Plot projectors on axis ax.

Parameters:

ax – matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_densities(ax=None, timesr2=False, fontsize: int = 8, **kwargs) → Any

Plot AE, PS and model densities on axis ax.

Parameters:

ax – matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_der_densities(ax=None, order=1, acc=4, fontsize=8, **kwargs) → Any

Plot the radial derivatives of the densities on axis ax. Used to analyze possible discontinuities or strong oscillations in r-space.

Parameters:

ax – matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_potentials(ax=None, fontsize: int = 8, **kwargs) → Any

Plot v_l and v_loc potentials on axis ax.

Parameters:

ax – matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_vtau(xscale='log', ax=None, fontsize: int = 8, **kwargs) → Any

Plot v_tau and v_tau(model+pseudo) potentials on axis ax.

Parameters:

• xscale – “log” to plot vtau in log scale or “linear”. For other options see matplotlib.

• ax – matplotlib.axes.Axes or None if a new figure should be created.

plot_tau(ax=None, yscale='log', fontsize: int = 8, **kwargs) → Any

Plot kinetic energy densities tauPS and tau(M+PS) on axis ax.

Parameters:

• yscale – “log” to plot tau in log scale or “linear”. For other options see matplotlib.

• ax – matplotlib.axes.Axes or None if a new figure should be created.

plot_der_potentials(ax=None, order=1, acc=4, fontsize: int = 8, **kwargs) → Any

Plot the derivatives of vl and vloc potentials on axis ax. Used to analyze the derivative discontinuity introduced by the RRKJ method at rc.

Parameters:

ax – matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_kene_vs_ecut(ax=None, fontsize: int = 8, **kwargs) → Any

Plot the convergence of the kinetic energy wrt ecut on axis ax.

Parameters:

ax – matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_atanlogder_econv(ax_list=None, fontsize: int = 6, **kwargs) → Any

Plot atan(logder) and the convergence of kinetic energy on the same figure.

Return: 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.
plotly	Try to convert mpl figure to plotly.

plot_den_formfact(ecut=120, ax=None, fontsize: int = 8, **kwargs) → Any

Plot the density form factor as a function of ecut in Ha.

Parameters:

ax – matplotlib.axes.Axes or None if a new figure should be created.

Return: 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.
plotly	Try to convert mpl figure to plotly.

plot_atomic_levels(ax=None, fontsize: int = 0, **kwargs) → Any

Plot atomic levels in Ha.

Parameters:

ax – matplotlib.axes.Axes or None if a new figure should be created.

Return: 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.
plotly	Try to convert mpl figure to plotly.

yield_figs(**kwargs)

Generate a predefined list of matplotlib figures with minimal input from the user.

write_notebook(nbpath=None)

Write a jupyter notebook to nbpath. If nbpath is None, a temporay file is created. Return path to the notebook. A typical template:

# Preable.
nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None)

#####################
# Put your code here
nb.cells.extend([
    nbv.new_markdown_cell("# This is a markdown cell"),
    nbv.new_code_cell("a = 1"),
])
#####################

# Call _write_nb_nbpath
return self._write_nb_nbpath(nb, nbpath)

abipy.ppcodes.oncv_plotter.oncv_make_open_notebook(outpath: str, foreground: bool = False, classic_notebook: bool = False, no_browser: bool = False) → int

Generate an ipython notebook and open it in the browser.

Parameters:

• foreground – By default, jupyter is executed in background and stdout, stderr are redirected to devnull. Use foreground to run the process in foreground

• classic_notebook – True to use the classic notebook instead of jupyter-lab (default)

• no_browser – Start the jupyter server to serve the notebook but don’t open the notebook in the browser. Use this option to connect remotely from localhost to the machine running the kernel

Return: system exit code.

Raise: RuntimeError if jupyter executable is not in $PATH

abipy.ppcodes.oncv_plotter.oncv_write_notebook(outpath: str, nbpath: str | None = None) → str

Write an ipython notebook to nbpath If nbpath is None, a temporay file is created. Return path to the notebook.

class abipy.ppcodes.oncv_plotter.MultiOncvPlotter

Bases: NotebookWriter

Object for comparing and plotting multiple pseudos.

Usage example:

plotter = MultiOncvPlotter.from_files(filepaths)
plotter.plot_atan_logders()

classmethod from_files(files: list[str]) → MultiOncvPlotter

Create an instance from a list of oncvpsp output files.

add_file(label: str, filepath: str) → None

Add a oncvps output file to the plotter with label

property plotters: list[OncvPlotter]

“List of registered Plotters.

property labels: list[str]

List of labels.

items()

List of plotters.

plot_atan_logders(ax_list=None, with_xlabel=True, xlims=None, ylims=None, fontsize: int = 8, **kwargs) → Any

Plot arctan of logder on ax_list for all pseudos.

Parameters:

ax_list – List of matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_radial_wfs(ax_list=None, what='bound_states', fontsize: int = 8, **kwargs) → Any

Plot AE and PS radial wavefunctions of ax_list for all pseudos.

Parameters:

• ax_list – List of matplotlib.axes.Axes or None if a new figure should be created.

• what – “bound_states” or “scattering_states”.

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.
plotly	Try to convert mpl figure to plotly.

plot_projectors(ax_list=None, fontsize: int = 8, **kwargs) → Any

Plot projectors on ax_list for all pseudos.

Parameters:

• ax_list – List of matplotlib.axes.Axes or None if a new figure should be created.

• ax – matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_densities(ax_list=None, timesr2=False, fontsize: int = 8, **kwargs) → Any

Plot AE, PS and model densities on ax_list for all pseudos.

Parameters:

• ax_list – List of matplotlib.axes.Axes or None if a new figure should be created.

• ax – matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_der_densities(ax_list=None, order=1, acc=4, fontsize=8, **kwargs) → Any

Plot the radial derivatives of the densities on ax_list for all pseudos. Used to analyze possible discontinuities or strong oscillations in r-space.

Parameters:

ax_list – List of matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_potentials(ax_list=None, fontsize: int = 8, **kwargs) → Any

Plot v_l and v_loc potentials on ax_list for all pseudos.

Parameters:

ax_list – List of matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_der_potentials(ax_list=None, order=1, acc=4, fontsize: int = 8, **kwargs) → Any

Plot the derivatives of vl and vloc potentials on ax_list for all pseudos. Used to analyze the derivative discontinuity introduced by the RRKJ method at rc.

Parameters:

ax_list – List of matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_kene_vs_ecut(ax_list=None, fontsize: int = 8, **kwargs) → Any

Plot the convergence of the kinetic energy wrt ecut on ax_list for all pseudos.

Parameters:

ax_list – List of matplotlib.axes.Axes or None if a new figure should be created.

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.
plotly	Try to convert mpl figure to plotly.

plot_atanlogder_econv(ax_mat=None, fontsize: int = 6, **kwargs) → Any

Plot atan(logder) and converge of kinetic energy on the same figure for all pseudos. Return: 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.
plotly	Try to convert mpl figure to plotly.

plot_den_formfact(ecut=120, ax_list=None, fontsize: int = 8, **kwargs) → Any

Plot the density form factor as a function of ecut in Ha on ax_list for all pseudos.

Parameters:

ax_list – List of matplotlib.axes.Axes or None if a new figure should be created.

Return: 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.
plotly	Try to convert mpl figure to plotly.

plot_atomic_levels(ax_list=None, fontsize: int = 8, **kwargs) → Any

Plot atomic levels in Ha for all pseudos.

Parameters:

ax_list – List of matplotlib.axes.Axes or None if a new figure should be created.

Return: 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.
plotly	Try to convert mpl figure to plotly.

yield_figs(**kwargs)

Generate a predefined list of matplotlib figures with minimal input from the user.

write_notebook(nbpath=None)

Write a jupyter notebook to nbpath. If nbpath is None, a temporay file is created. Return path to the notebook. A typical template:

# Preable.
nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None)

#####################
# Put your code here
nb.cells.extend([
    nbv.new_markdown_cell("# This is a markdown cell"),
    nbv.new_code_cell("a = 1"),
])
#####################

# Call _write_nb_nbpath
return self._write_nb_nbpath(nb, nbpath)

abipy.ppcodes.oncv_plotter.psp8_get_densities(path, fc_file=None, ae_file=None, plot=False)

Extract AE-core, AE-valence and PS-valence from a psp8 file. Optionally write .fc and .AE file in format suitable for AIM and cut3d Hirshfeld code.

Parameters:

• path – path of the psp8 file

• fc_file – File-like object to .fc. and .AE file Set to None if files are now wanted.

• ae_file – File-like object to .fc. and .AE file Set to None if files are now wanted.

• plot – If true, call matplotlib to plot densities.

Returns:

(rmesh, psval, aeval, aecore)

Densities are multiplied by 4 pi i.e. int aecore * r**2 dr ~= N_core

Return type:

namedtuple with numpy arrays

Warning

The densities do not integrate exactly to the number of core/valence electrons. in particular the valence charge in elements with large Z as valence electrons are more delocalized and the finite radial mesh does not capture the contribution due to the tail. Client code is responsible for extrapolating the valence charge if needed. The error in the integral of the core charge is usually much smaller and should be ok for qualitative analysis.

ppgen Module

Interface for pseudopotential generators.

class abipy.ppcodes.ppgen.Status

Bases: int

An integer representing the status of the ‘PseudoGenerator`.

classmethod as_status(obj: Status | str) → Status

Convert obj into Status.

classmethod from_string(s: str) → Status

Return an instance from its string representation.

class abipy.ppcodes.ppgen.OncvGenerator(input_str: str, calc_type: str, use_mgga: bool, workdir: str | None = None)

Bases: _PseudoGenerator

This object receives an input file for oncvpsp, a string that defines the type of calculation (scalar-relativistic, …) runs the code in a temporary directory and provides methods to validate/analyze/plot the final results.

retcode

Retcode of oncvpsp

classmethod from_file(path: str, calc_type: str, use_mgga: bool, workdir: str | None = None) → OncvGenerator

Build the object from a file containing the input parameters.

check_status()

Check the status of the run, set and return self.status attribute.