Expand cbar limits to 0 if very close

doped/chemical_potentials.py

@@ -2621,6 +2621,7 @@ def plot_chempot_heatmap(
  dependent_element: Optional[Union[str, Element]] = None,
  xlim: Optional[tuple[float, float]] = None,
  ylim: Optional[tuple[float, float]] = None,
+ cbar_range: Optional[tuple[float, float]] = None,
  padding: Optional[float] = None,
  title: Optional[Union[str, bool]] = None,
  label_positions: Optional[Union[list[float], dict[str, float], bool]] = None,
@@ -2649,7 +2650,6 @@ def plot_chempot_heatmap(
  # TODO: Code in this function (particularly label position handling and intersections) should be
  # able to be made more succinct, and also modularise a bit?
  # TODO: Expand axes slightly if labels touching bbox
- # TODO: Extend cbar so ticks at both ends?
  # TODO: Can use `yoffsets` parameter to shift the labels for vertical lines, to allow more
  # control; implement this (removes need for np.unique() call)), units = plot y units
  cpd = ChemicalPotentialDiagram(list(self.intrinsic_phase_diagram.entries))
@@ -2688,7 +2688,7 @@ def plot_chempot_heatmap(
  grid_x, grid_y = np.mgrid[x_min:x_max:300j, y_min:y_max:300j] # type: ignore
  grid_points = np.vstack([grid_x.ravel(), grid_y.ravel()]).T
 
- # Delaunay triangulation to get points inside the hull:
+ # Delaunay triangulation to get points inside the stability hull:
  delaunay = Delaunay(hull.points[hull.vertices])
  inside_hull = delaunay.find_simplex(grid_points) >= 0
  points_inside = grid_points[inside_hull]
@@ -2701,21 +2701,17 @@ def plot_chempot_heatmap(
  fig, ax = plt.subplots()
  mesh_x, x_indices = np.unique(points_inside[:, 0], return_inverse=True)
  mesh_y, y_indices = np.unique(points_inside[:, 1], return_inverse=True)
+ mesh_z = np.full((len(mesh_y), len(mesh_x)), np.nan) # Create the mesh grid, init with NaNs
+ mesh_z[y_indices, x_indices] = values_inside # populate the grid
 
- # Step 2: Create the mesh grid and initialize with NaNs
- mesh_z = np.full((len(mesh_y), len(mesh_x)), np.nan)
-
- # Step 3: Populate the mesh grid
- mesh_z[y_indices, x_indices] = values_inside
-
+ vmin = cbar_range[0] if cbar_range else None
+ vmax = cbar_range[1] if cbar_range else None
+ if vmax is None and np.isclose(np.nanmax(mesh_z), 0, atol=3e-2):
+ vmax = 0 # extend to 0, as sometimes cutoff at -0.01 eV etc
  dep_mu = ax.pcolormesh(
- mesh_x,
- mesh_y,
- mesh_z,
- rasterized=True,
- cmap=cm.batlow,
- shading="auto",
+ mesh_x, mesh_y, mesh_z, rasterized=True, cmap=cm.batlow, shading="auto", vmax=vmax, vmin=vmin
  )
+
  cbar = fig.colorbar(dep_mu)
 
  x_range = abs(x_max - x_min)

tests/test_thermodynamics.py

@@ -474,7 +474,7 @@ def test_initialisation_and_attributes(self):
  def test_DefectsParser_thermo_objs(self):
  """
  Test the `DefectThermodynamics` objects created from the
- `DefectsParser.get_defect_thermodynamics()` method.
+ ``DefectsParser.get_defect_thermodynamics()`` method.
  """
  for defect_thermo, name in [
  (self.CdTe_defect_thermo, "CdTe_defect_thermo"),