Update default options for consistency

doped/core.py

@@ -1284,16 +1284,19 @@ def sc_entry_energy(self):
 
  def plot_site_displacements(
  self,
- separated_by_direction: Optional[bool] = False,
- relative_to_defect: Optional[bool] = False,
+ separated_by_direction: bool = False,
+ relative_to_defect: bool = False,
  vector_to_project_on: Optional[list] = None,
- use_plotly: Optional[bool] = False,
- mpl_style_file: Optional[PathLike] = "",
+ use_plotly: bool = False,
+ style_file: Optional[PathLike] = "",
  ):
  """
  Plot the site displacements as a function of distance from the defect
  site.
 
+ Set ``use_plotly = True`` to get an interactive ``plotly`` plot, useful
+ for analysis!
+
  Args:
  separated_by_direction (bool):
  Whether to plot the site displacements separated by the
@@ -1308,8 +1311,9 @@ def plot_site_displacements(
  (e.g. [0, 0, 1]). Defaults to None (e.g. the displacements are calculated
  in the cartesian basis x, y, z).
  use_plotly (bool):
- Whether to use plotly (True) or matplotlib (False).
- mpl_style_file (PathLike):
+ Whether to use ``plotly`` (``True``) or ``matplotlib`` (``False``).
+ Defaults to ``False``. Set to ``True`` to get an interactive plot.
+ style_file (PathLike):
  Path to a matplotlib style file to use for the plot. If None,
  uses the default doped style file.
  """
@@ -1321,7 +1325,7 @@ def plot_site_displacements(
  relative_to_defect=relative_to_defect,
  vector_to_project_on=vector_to_project_on,
  use_plotly=use_plotly,
- style_file=mpl_style_file,
+ style_file=style_file,
  )
 
 

doped/utils/displacements.py

@@ -36,7 +36,7 @@
 def calc_site_displacements(
  defect_entry: DefectEntry,
  vector_to_project_on: Optional[list] = None,
- relative_to_defect: Optional[bool] = False,
+ relative_to_defect: bool = False,
 ) -> dict:
  """
  Calculates the site displacements in the defect supercell, relative to the
@@ -79,7 +79,7 @@ def calc_site_displacements(
  disp_dict["Displacement projected along vector"] = []
  disp_dict["Displacement perpendicular to vector"] = []
  for i, site in enumerate(defect_sc_with_site):
- # print(i, site.specie, site.frac_coords)
+ # print(i, site.specie, site.frac_coords) # debugging
  bulk_sc_index = mappings_dict[i] # Map to bulk sc
  bulk_site = bulk_sc[bulk_sc_index] # Get site in bulk sc
  # Calculate displacement (need to account for pbc!)
@@ -88,7 +88,7 @@ def calc_site_displacements(
  disp = bulk_sc.lattice.get_cartesian_coords(frac_disp) # in Angstroms
  # Distance to defect site (last site in defect sc)
  distance = defect_sc_with_site.get_distance(i, defect_site_index) # len(defect_sc_with_site) - 1)
- # print(i, displacement, np.linalg.norm(abs_disp), "Distance:", distance)
+ # print(i, displacement, np.linalg.norm(abs_disp), "Distance:", distance) # debugging
  disp_dict["Index (defect)"].append(i)
  disp_dict["Displacement"].append(disp)
  disp_dict["Distance to defect"].append(distance)
@@ -198,15 +198,18 @@ def calc_site_displacements(
 
 def plot_site_displacements(
  defect_entry: DefectEntry,
- separated_by_direction: Optional[bool] = False,
- relative_to_defect: Optional[bool] = False,
+ separated_by_direction: bool = False,
+ relative_to_defect: bool = False,
  vector_to_project_on: Optional[list] = None,
- use_plotly: Optional[bool] = True,
+ use_plotly: bool = False,
  style_file: Optional[PathLike] = None,
 ):
  """
  Plots site displacements around a defect.
 
+ Set ``use_plotly = True`` to get an interactive ``plotly``
+ plot, useful for analysis!
+
  Args:
  defect_entry (DefectEntry): DefectEntry object
  separated_by_direction (bool):
@@ -220,15 +223,17 @@ def plot_site_displacements(
  (tensile strain). Uses the *relaxed* defect position as reference.
  vector_to_project_on (bool):
  Direction to project the site displacements along
- (e.g. [0, 0, 1]). Defaults to None (e.g. the displacements are calculated
- in the cartesian basis x, y, z).
+ (e.g. [0, 0, 1]). Defaults to None (e.g. the displacements
+ are calculated in the cartesian basis x, y, z).
  use_plotly (bool):
- Whether to use Plotly for plotting. Default is True.
+ Whether to use ``plotly`` for plotting. Default is ``False``.
+ Set to ``True`` to get an interactive plot.
  style_file (PathLike):
- Path to matplotlib style file. if not set, will use the ``doped`` default style.
+ Path to matplotlib style file. if not set, will use the
+ ``doped`` default style.
 
  Returns:
- Plotly or matplotlib figure.
+ ``plotly`` or ``matplotlib`` ``Figure``.
  """
 
  def _mpl_plot_total_disp(
@@ -488,24 +493,35 @@ def _plotly_plot_total_disp(
 
 def calc_displacements_ellipsoid(
  defect_entry: DefectEntry,
- plot_ellipsoid: Optional[bool] = False, # Option to plot the ellipsoid
- plot_anisotropy: Optional[bool] = False, # Option to plot anisotropy of ellipsoid radii
- use_plotly: Optional[bool] = True,
- quantile=0.8, # Quantile threshold for displacement norms (0 to 1). Default is 0.8.
+ plot_ellipsoid: bool = False,
+ plot_anisotropy: bool = False,
+ use_plotly: bool = False,
+ quantile=0.8,
 ):
  """
  Calculate displacements around a defect site and fit an ellipsoid to these
  displacements.
 
- Parameters:
- - defect_entry (DefectEntry): An object representing the defect in the crystal structure.
- - plot_anisotropy (bool, optional): If True, plot the anisotropy of the ellipsoid radii.
- - plot_ellipsoid (bool, optional): If True, plot the fitted ellipsoid in the crystal lattice.
- - quantile (float): The quantile threshold for selecting significant displacements (between 0 and 1).
+ Set ``use_plotly = True`` to get an interactive ``plotly``
+ plot, useful for analysis!
+
+ Args:
+ defect_entry (DefectEntry): ``DefectEntry`` object.
+ plot_ellipsoid (bool):
+ If True, plot the fitted ellipsoid in the crystal lattice.
+ plot_anisotropy (bool):
+ If True, plot the anisotropy of the ellipsoid radii.
+ use_plotly (bool):
+ Whether to use ``plotly`` for plotting. Default is ``False``.
+ Set to ``True`` to get an interactive plot.
+ quantile (float):
+ The quantile threshold for selecting significant displacements
+ (between 0 and 1). Default is 0.8.
 
  Returns:
- - (ellipsoid_center, ellipsoid_radii, ellipsoid_rotation): A tuple containing the ellipsoid's center,
- radii, and rotation matrix, or (None, None, None) if fitting was unsuccessful.
+ - (ellipsoid_center, ellipsoid_radii, ellipsoid_rotation):
+ A tuple containing the ellipsoid's center, radii, and rotation matrix,
+ or ``(None, None, None)`` if fitting was unsuccessful.
  """
  if use_plotly and not plotly_installed:
  warnings.warn("Plotly not installed, using matplotlib instead")
@@ -795,9 +811,9 @@ def _mpl_plot_anisotropy(ellipsoid_radii, disp_df, threshold):
  fig, axs = plt.subplots(1, 2, figsize=(14, 6))
 
  # Part 1: Displacement Distribution Box Plot
- axs[0].boxplot(disp_df["Displacement norm"], vert=True, patch_artist=True)
- axs[0].set_title("Displacement norm's distribution")
- axs[0].set_ylabel("Displacement norm (Å)")
+ axs[0].boxplot(disp_df["Displacement Norm"], vert=True, patch_artist=True)
+ axs[0].set_title("Displacement Norm Distribution")
+ axs[0].set_ylabel("Displacement Norm (Å)")
  axs[0].grid(False)
  axs[0].xaxis.set_visible(False) # Hide x-axis labels for box plot
 
@@ -822,12 +838,12 @@ def _mpl_plot_anisotropy(ellipsoid_radii, disp_df, threshold):
 
  # Add colorbar
  cbar = plt.colorbar(scatter, ax=axs[1])
- cbar.set_label("The longest radius of ellipsoid")
+ cbar.set_label("Ellipsoid Maximum Radius (Å)")
 
  # Set titles and labels
- axs[1].set_title(f"Anisotropy plot (threshold={np.round(threshold, 3)}Å)")
- axs[1].set_xlabel("The 2nd longest radius / the longest radius of ellipsoid")
- axs[1].set_ylabel("The shortest radius / the longest radius of ellipsoid")
+ axs[1].set_title(f"Anisotropy (Threshold = {threshold:.3f} Å)")
+ axs[1].set_xlabel("2nd-Largest Radius / Largest Radius")
+ axs[1].set_ylabel("Shortest Radius / Largest Radius")
  axs[1].set_xlim([0, 1])
  axs[1].set_ylim([0, 1])
  axs[1].grid(False)
@@ -841,8 +857,8 @@ def _plotly_plot_anisotropy(ellipsoid_radii, disp_df, threshold):
  rows=1,
  cols=2,
  subplot_titles=[
- "Displacement Norm distribution",
- f"Anisotropy plot (threshold={np.round(threshold, 3)}Å)",
+ "Displacement Norm Distribution",
+ f"Anisotropy (Threshold = {threshold:.3f} Å)",
  ],
  column_widths=[0.5, 0.5],
  )
@@ -892,7 +908,7 @@ def _plotly_plot_anisotropy(ellipsoid_radii, disp_df, threshold):
  "opacity": 0.5,
  "color": anisotropy_info_df["the_longest_radius"], # Set color according to column "a"
  "colorscale": "rainbow",
- "colorbar": {"title": "The longest radius of ellipsoid", "titleside": "right"},
+ "colorbar": {"title": "Ellipsoid Maximum Radius (Å)", "titleside": "right"},
  },
  text=anisotropy_info_df["the_longest_radius"],
  hoverinfo="text",
@@ -907,7 +923,7 @@ def _plotly_plot_anisotropy(ellipsoid_radii, disp_df, threshold):
 
  # Add frame to Anisotropy plot
  fig.update_xaxes(
- title_text="The 2nd longest radius / the longest radius of ellipsoid",
+ title_text="2nd-Largest Radius / Largest Radius",
  range=[0, 1],
  row=1,
  col=2,
@@ -918,7 +934,7 @@ def _plotly_plot_anisotropy(ellipsoid_radii, disp_df, threshold):
  mirror=True,
  )
  fig.update_yaxes(
- title_text="The shortest radius / the longest radius of ellipsoid",
+ title_text="Shortest Radius / Largest Radius",
  range=[0, 1],
  row=1,
  col=2,
@@ -989,7 +1005,7 @@ def _shift_defect_site_to_center_of_the_supercell(sites_frac_coords, defect_frac
  "Species": [],
  "Species_with_index": [],
  "Displacement": [],
- "Displacement norm": [],
+ "Displacement Norm": [],
  "Distance to defect": [],
  "X sites in cartesian coordinate (defect)": [],
  "Y sites in cartesian coordinate (defect)": [],
@@ -1016,7 +1032,7 @@ def _shift_defect_site_to_center_of_the_supercell(sites_frac_coords, defect_frac
 
  disp_dict["Index (defect)"].append(i)
  disp_dict["Displacement"].append(disp)
- disp_dict["Displacement norm"].append(np.linalg.norm(disp, ord=2))
+ disp_dict["Displacement Norm"].append(np.linalg.norm(disp, ord=2))
  disp_dict["Distance to defect"].append(distance)
  disp_dict["Species_with_index"].append(f"{site.specie.name}({i})")
  disp_dict["Species"].append(site.specie.name)
@@ -1061,7 +1077,7 @@ def _shift_defect_site_to_center_of_the_supercell(sites_frac_coords, defect_frac
  disp_dict["Species"],
  disp_dict["Species_with_index"],
  disp_dict["Displacement"],
- disp_dict["Displacement norm"],
+ disp_dict["Displacement Norm"],
  disp_dict["Distance to defect"],
  disp_dict["X sites in cartesian coordinate (defect)"],
  disp_dict["Y sites in cartesian coordinate (defect)"],
@@ -1072,13 +1088,10 @@ def _shift_defect_site_to_center_of_the_supercell(sites_frac_coords, defect_frac
  disp_df = pd.DataFrame(disp_dict)
 
  # Calculate the threshold for displacement norm, ensuring it's at least 0.05
- threshold = max(disp_df["Displacement norm"].quantile(quantile), 0.05)
+ threshold = max(disp_df["Displacement Norm"].quantile(quantile), 0.05)
 
  # Filter the DataFrame to get points where the displacement norm exceeds the threshold
- displacement_norm_over_threshold = disp_df[disp_df["Displacement norm"] > threshold]
-
- # Print the threshold for debugging purposes
- print(f"threshold: {threshold}")
+ displacement_norm_over_threshold = disp_df[disp_df["Displacement Norm"] > threshold]
 
  # Extract the Cartesian coordinates of the points that are over the threshold
  points = displacement_norm_over_threshold[