Add sampling region shading to eFNV plots

doped/analysis.py

@@ -1284,8 +1284,9 @@ def get_stdrd_metadata(self):
             self.defect_vr = get_vasprun(defect_vr_path)
 
         run_metadata = {  # TODO: Add check that incars, kpoints and potcars are compatible here
-            "defect_incar": self.defect_vr.incar,
-            "bulk_incar": self.bulk_vr.incar,
+            # incars need to be as dict without module keys otherwise not JSONable:
+            "defect_incar": {k: v for k, v in self.defect_vr.incar.as_dict().items() if "@" not in k},
+            "bulk_incar": {k: v for k, v in self.bulk_vr.incar.as_dict().items() if "@" not in k},
             "defect_kpoints": self.defect_vr.kpoints,
             "bulk_kpoints": self.bulk_vr.kpoints,
             "defect_potcar_symbols": self.defect_vr.potcar_spec,

doped/corrections.py

@@ -451,16 +451,29 @@ def get_kumagai_correction(
         fig = spp.plt.gcf()
         ax = fig.gca()
 
-        # reformat plot slightly
+        # reformat plot slightly:
+        x_lims = ax.get_xlim()
+        y_lims = ax.get_ylim()
+        # shade in sampling region:
+        spp.plt.fill_between(
+            [spp.defect_region_radius, x_lims[1]],
+            *y_lims,
+            color="purple",
+            alpha=0.15,
+            label="Sampling Region",
+        )
+        spp.plt.ylim(*y_lims)  # reset y-lims after fill_between
+
+        # update legend:
         handles, labels = ax.get_legend_handles_labels()
         labels = [
             label.replace("point charge", "Point Charge (PC)").replace(
                 "potential difference", r"$\Delta V$"
             )
             for label in labels
         ]
-        # add entry for dashed red line
 
+        # add entry for dashed red line:
         handles += [Line2D([0], [0], **spp._mpl_defaults.hline)]
         labels += [
             rf"Avg. $\Delta V$ = {spp.ave_pot_diff:.3f} V",

tests/test_corrections.py

@@ -260,9 +260,9 @@ def test_plot_kumagai_custom(self):
         """
         mpl.pyplot.clf()
         _corr, fig = get_kumagai_correction(self.F_O_1_entry, dielectric=[40.7, 40.7, 25.2], plot=True)
-        # add shading to left part of plot (10 Angstrom on):
+        # add shading to plot:
         ax = fig.gca()
-        ax.axvspan(10, 100, alpha=0.2, color="purple")
+        ax.axvspan(5, 100, alpha=0.2, color="yellow")
 
         return fig