Add methods to plot tau and vtau

abipy/ppcodes/oncv_parser.py

@@ -511,6 +511,43 @@ def densities(self) -> dict[str, RadialFunction]:
  rhoM=RadialFunction("Model charge", rho_data[:, 0], rho_data[:, 3])
  )
 
+ @lazy_property
+ def kin_densities(self) -> dict[str, RadialFunction]:
+ """
+ Dictionary with Kinetic energy densities on the radial mesh.
+ """
+ if not self.is_metapsp:
+ raise ValueEror("kin_densities are only available in pseudos generated with metapsp")
+
+ # Metagga taups and taumodps
+ #!t 0.0200249 2.9590E+02 6.4665E+02
+ rho_data = self._grep("!t").data
+
+ return dict(
+ tau_ps=RadialFunction("Tau Pseudo", rho_data[:, 0], rho_data[:, 1]),
+ tau_modps=RadialFunction("Tau Model + Pseudo", rho_data[:, 0], rho_data[:, 2]),
+ )
+
+ @lazy_property
+ def vtaus(self) -> dict[str, RadialFunction]:
+ """
+ Dictionary with Vtau pototentials on the radial mesh.
+ """
+ if not self.is_metapsp:
+ raise ValueEror("kin_densities are only available in pseudos generated with metapsp")
+
+ # plot "<grep '!vt' t1" using 2:3 title "VtauAE" with lines ls 1,\
+ # "<grep '!vt' t1" using 2:4 title "Vtau(M+PS)" with lines ls 9
+
+ # !vt 0.1000394 4.1827E-03 1.9061E-02
+ # !vt 0.1024657 4.5435E-03 1.9061E-02
+ rho_data = self._grep("!vt").data
+
+ return dict(
+ vtau_ae=RadialFunction("Vtau AE", rho_data[:, 0], rho_data[:, 1]),
+ vtau_modps=RadialFunction("VTau Model + Pseudo", rho_data[:, 0], rho_data[:, 2]),
+ )
+
  @lazy_property
  def radial_wfs(self) -> AePsNamedTuple:
  """

abipy/ppcodes/oncv_plotter.py

@@ -101,9 +101,9 @@ def _add_rc_vlines_ax(self, ax, with_lloc=False) -> None:
  ax._custom_rc_lines.append((self.parser.rc5, color))
 
  def plotly_atan_logders(self, *args, **kwargs):
- mpl_fig = self.plot_atan_logders(*args, show=False, **kwargs)
+ """Generate plotly figure from matplotly."""
  from plotly.tools import mpl_to_plotly
- return mpl_to_plotly(mpl_fig)
+ return mpl_to_plotly(self.plot_atan_logders(*args, show=False, **kwargs))
 
  @add_fig_kwargs
  def plot_atan_logders(self, ax=None, with_xlabel=True,
@@ -156,6 +156,10 @@ def _get_ae_ps_wfs(self, what) -> tuple:
  raise ValueError(f"Invalid value for {what=}")
  return ae_wfs, ps_wfs
 
+ def plotly_radial_wfs(self, *args, **kwargs):
+ """Generate plotly figure from matplotly."""
+ from plotly.tools import mpl_to_plotly
+ return mpl_to_plotly(self.plot_radial_wfs(*args, show=False, **kwargs))
 
  @add_fig_kwargs
  def plot_radial_wfs(self, ax=None, what="bound_states",
@@ -175,7 +179,7 @@ def plot_radial_wfs(self, ax=None, what="bound_states",
  ps_wf, l, k = ps_wfs[nlk], nlk.l, nlk.k
 
  if what == "bound_states":
- #  # Show position of the last peak.
+ # Show position of the last peak.
  s, marker = 10, "^"
  ae_peaks = ae_wf.get_peaks()
  style = dict(color=self.color_l[l], s=s, marker=marker)
@@ -197,6 +201,11 @@ def plot_radial_wfs(self, ax=None, what="bound_states",
 
  return fig
 
+ def plotly_projectors(self, *args, **kwargs):
+ """Generate plotly figure from matplotly."""
+ from plotly.tools import mpl_to_plotly
+ return mpl_to_plotly(self.plot_projects(*args, show=False, **kwargs))
+
  @add_fig_kwargs
  def plot_projectors(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
  """
@@ -226,6 +235,11 @@ def plot_projectors(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
 
  return fig
 
+ def plotly_densities(self, *args, **kwargs):
+ """Generate plotly figure from matplotly."""
+ from plotly.tools import mpl_to_plotly
+ return mpl_to_plotly(self.plot_densities(*args, show=False, **kwargs))
+
  @add_fig_kwargs
  def plot_densities(self, ax=None, timesr2=False, fontsize: int = 8, **kwargs) -> Figure:
  """
@@ -248,6 +262,11 @@ def plot_densities(self, ax=None, timesr2=False, fontsize: int = 8, **kwargs) ->
  )
  return fig
 
+ def plotly_der_densities(self, *args, **kwargs):
+ """Generate plotly figure from matplotly."""
+ from plotly.tools import mpl_to_plotly
+ return mpl_to_plotly(self.plot_der_densities(*args, show=False, **kwargs))
+
  @add_fig_kwargs
  def plot_der_densities(self, ax=None, order=1, acc=4, fontsize=8, **kwargs) -> Figure:
  """
@@ -276,6 +295,11 @@ def plot_der_densities(self, ax=None, order=1, acc=4, fontsize=8, **kwargs) -> F
  )
  return fig
 
+ def plotly_potentials(self, *args, **kwargs):
+ """Generate plotly figure from matplotly."""
+ from plotly.tools import mpl_to_plotly
+ return mpl_to_plotly(self.plot_potentials(*args, show=False, **kwargs))
+
  @add_fig_kwargs
  def plot_potentials(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
  """
@@ -298,6 +322,65 @@ def plot_potentials(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
 
  return fig
 
+ def plotly_vtau(self, *args, **kwargs):
+ """Generate plotly figure from matplotly."""
+ from plotly.tools import mpl_to_plotly
+ return mpl_to_plotly(self.plot_vtau(*args, show=False, **kwargs))
+
+ def plot_vtau(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
+ """
+ Plot v_tau and v_tau(model+pseudo) potentials on axis ax.
+
+ Args:
+ ax: |matplotlib-Axes| or None if a new figure should be created.
+ """
+ ax, fig, plt = get_ax_fig_plt(ax)
+
+ for key, pot in self.parser.vtaus.items():
+ mode = "ae" if key == "vtau_ae" else "ps"
+ ax.plot(pot.rmesh, pot.values,
+ label=pot.name,
+ **self._mpl_opts_laeps(0, mode))
+
+ self.decorate_ax(ax, xlabel="r (Bohr)", ylabel="Vtaus (Ha / a_B)",
+ #title="Ion Pseudopotentials",
+ fontsize=fontsize,
+ )
+ self._add_rc_vlines_ax(ax, with_lloc=True)
+
+ def plotly_tau(self, *args, **kwargs):
+ """Generate plotly figure from matplotly."""
+ from plotly.tools import mpl_to_plotly
+ return mpl_to_plotly(self.plot_tau(*args, show=False, **kwargs))
+
+ def plot_tau(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
+ """
+ Plot kinetic energy densities tauPS and tau(M+PS) on axis ax.
+
+ Args:
+ ax: |matplotlib-Axes| or None if a new figure should be created.
+ """
+ ax, fig, plt = get_ax_fig_plt(ax)
+
+ for key, den in self.parser.kin_densities.items():
+ #mode = "ae" if key == "tau_ps" else "ps"
+ ax.plot(den.rmesh, den.values,
+ label=den.name)
+ #**self._mpl_opts_laeps(0, mode))
+
+ self.decorate_ax(ax, xlabel="r (Bohr)", ylabel="Kinetic energy densities",
+ #title="Ion Pseudopotentials",
+ fontsize=fontsize,
+ )
+ self._add_rc_vlines_ax(ax, with_lloc=True)
+
+ return fig
+
+ def plotly_der_potentials(self, *args, **kwargs):
+ """Generate plotly figure from matplotly."""
+ from plotly.tools import mpl_to_plotly
+ return mpl_to_plotly(self.plot_der_potentials(*args, show=False, **kwargs))
+
  @add_fig_kwargs
  def plot_der_potentials(self, ax=None, order=1, acc=4, fontsize: int = 8, **kwargs) -> Figure:
  """
@@ -329,6 +412,11 @@ def plot_der_potentials(self, ax=None, order=1, acc=4, fontsize: int = 8, **kwar
 
  return fig
 
+ def plotly_kene_vs_ecut(self, *args, **kwargs):
+ """Generate plotly figure from matplotly."""
+ from plotly.tools import mpl_to_plotly
+ return mpl_to_plotly(self.plot_kene_vs_ecut(*args, show=False, **kwargs))
+
  @add_fig_kwargs
  def plot_kene_vs_ecut(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
  """
@@ -356,6 +444,11 @@ def plot_kene_vs_ecut(self, ax=None, fontsize: int = 8, **kwargs) -> Figure:
 
  return fig
 
+ def plotly_atanlogder_econv(self, *args, **kwargs):
+ """Generate plotly figure from matplotly."""
+ from plotly.tools import mpl_to_plotly
+ return mpl_to_plotly(self.plot_atan_logder_econv(*args, show=False, **kwargs))
+
  @add_fig_kwargs
  def plot_atanlogder_econv(self, ax_list=None, fontsize: int = 6, **kwargs) -> Figure:
  """
@@ -483,6 +576,10 @@ def yield_figs(self, **kwargs): # pragma: no cover
  for order in [1, 2, 3, 4]:
  yield self.plot_der_densities(order=order, show=False)
 
+ if self.parser.is_metapsp:
+ yield self.plot_vtau(show=False)
+ yield self.plot_tau(show=False)
+
  def write_notebook(self, nbpath=None):
  return oncv_make_open_notebook(self.parser.filepath)
 

abipy/scripts/oncv.py

@@ -79,6 +79,7 @@ def oncv_plot(options) -> int:
 
  out_path = _find_oncv_output(options.filepath)
  plotter = OncvPlotter.from_file(out_path)
+
  #plotter.plotly_atan_logders().show()
  #return 0